Technical Guide

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Contributing to SOPS

H3ABioNet welcomes contributions from everyone. Here are a few guidelines and instructions if you’re thinking of helping with the curation of SOPS.

Getting started

Install jekyll

• Make sure you have jekyll 2.4.0 or greater installed. You can find information on how to install jekyll here

Fork project repo

• After following the jekyll installation guide, Go to the H3ABionet-SOPs repository on Github here and click on Fork. Fork will create a copy of the repository in your Github account so that you can make changes to the project

Clone repo

• Go to your own Github repository and you will see a repository named H3ABionet-SOPs. Make a local copy of it on your computer by hitting the clone button
• Copy the Https URL, Open your terminal or git bash window and Change directory to where you want to create a copy of this project
• Run git clone appending the Https URL, looks like git clone https://github.com/userid/H3ABionet-SOPs.git where userid is your github username. This will automatically clone this repository. You now have a local copy on your computer.The working directory on your computer will have the same name as the remote repository on Github, H3ABionet-SOPs
• Add your fork to git’s remotes:
  • If you use SSH authentication: git remote add <your username> git@github.com:<your username>/H3ABionet-SOPs.git.
  • Otherwise: git remote add <your username>https://github.com/<your username>/H3ABionet-SOPs.git.

Make edits to the SOPs

• Switch into S0Ps directory, cd H3ABionet-SOPs.
• Using your favorite text editor make changes to the code and files as you deem necessary

Test your changes locally

• Build a local copy of site in your computer and view from your own browser as below:
  • At the prompt, simply run bundle
  • Run bundle exec jekyll serve to start the preview server
  • Visit localhost:4000 in your browser to preview the site

Commit

• Run git init command
• Run git status to see the current status of your local repo, showing that there are changes not staged to be committed with the modified files in red
• Run git add . to add these changes
• Re-run git status, your changes have now been staged and are ready to be committed
• Now run git commit -m to commit these changes. Remember to describe the specific changes you made in the git commit message
• Run git status again to check that everything is up to date

Push changes to your fork

• We can now push our code to the forked repository. Before we do this, run git remote -v to crosscheck that the remote repository on Github our local repository is connected to is indeed the forked repo
• Run git push origin master to push our changes to this repository
• Check that your remote repository has updated on Github

Submit Pull Requests

• You’re now all ready to submit the improvements/changes you’ve made to the project’s maintainers for approval
• Create a pull request against master, and a contributor will come by and review your submission. They may ask for some changes, and hopefully your contribution will be merged to the master branch!

Communication

If you need any help contributing to SOPs, several contributors are available